Genomics Reporting Implementation Guide
3.0.0 - STU3 International flag

This page is part of the Genetic Reporting Implementation Guide (v3.0.0: STU3) based on FHIR (HL7® FHIR® Standard) R4. This is the current published version in its permanent home (it will always be available at this URL). For a full list of available versions, see the Directory of published versions

Table of Contents

.. 0 Table of Contents
... 1 Home Page
... 2 Genomic Background
... 3 General Genomic Reporting
... 4 Variant Reporting
... 5 Pharmacogenomic Reporting
... 6 Somatic Reporting
... 7 Histocompatibility and Immunogenetic Reporting
... 8 Genomic Operations
... 9 Useful Downloads
... 10 Appendix A: Relation to v2 reporting
... 11 Appendix B: Clinical Genomic Apps
... 12 Appendix C: HL7 Domain Analysis Model
... 13 Appendix D: Query Guidance
... 14 Appendix E: External Coding Systems
... 15 Appendix F: Conversion from FHIR Core STU3
... 16 Appendix G: Molecular Sequence
... 17 Appendix H: Grouping Guidance
... 18 Appendix I: Glossary
... 19 Change Log
... 20 Artifacts Summary
.... 20.1 Find Population Diagnostic Implications
.... 20.2 Find Population Molecular Consequences
.... 20.3 Find Population Specific Haplotypes
.... 20.4 Find Population Specific Variants
.... 20.5 Find Population Structural Intersecting Variants
.... 20.6 Find Population Structural Subsuming Variants
.... 20.7 Find Population Treatment Implications
.... 20.8 Find Study Metadata
.... 20.9 Find Subject Diagnostic Implications
.... 20.10 Find Subject Haplotypes
.... 20.11 Find Subject Molecular Consequences
.... 20.12 Find Subject Specific Haplotypes
.... 20.13 Find Subject Specific Variants
.... 20.14 Find Subject Structural Intersecting Variants
.... 20.15 Find Subject Structural Subsuming Variants
.... 20.16 Find Subject Treatment Implications
.... 20.17 Find Subject Variants
.... 20.18 Genomic Base
.... 20.19 Genomic Finding
.... 20.20 Genomic Implication
.... 20.21 Diagnostic Implication
.... 20.22 Followup Recommendation
.... 20.23 Genomic Data File
.... 20.24 Genomic Report
.... 20.25 Genomic Study
.... 20.26 Genomic Study Analysis
.... 20.27 Genotype
.... 20.28 Haplotype
.... 20.29 Medication Recommendation
.... 20.30 Molecular Biomarker
.... 20.31 Molecular Consequence
.... 20.32 Sequence Phase Relationship
.... 20.33 Therapeutic Implication
.... 20.34 Variant
.... 20.35 Coded Annotation
.... 20.36 Annotation Code
.... 20.37 Genomic Report Note
.... 20.38 Genomic Risk Assessment
.... 20.39 Genomic Study Analysis Change Type
.... 20.40 Genomic Study Analysis Device
.... 20.41 Genomic Study Analysis Extension
.... 20.42 Genomic Study Analysis Focus
.... 20.43 Genomic Study Analysis Genome Build
.... 20.44 Genomic Study Analysis Input
.... 20.45 Genomic Study Analysis Method Type
.... 20.46 Genomic Study Analysis Metrics
.... 20.47 Genomic Study Analysis Output
.... 20.48 Genomic Study Analysis Protocol Performed
.... 20.49 Genomic Study Analysis Regions
.... 20.50 Genomic Study Analysis Source Class
.... 20.51 Genomic Study Analysis Specimen
.... 20.52 Genomic Study Analysis Title
.... 20.53 Genomic Study Reference
.... 20.54 Genomic Study Referrer Extension
.... 20.55 Medication Assessed reference to a FHIR resource
.... 20.56 Recommended Action
.... 20.57 Related Artifact for Observation component
.... 20.58 Repeat Motif Order
.... 20.59 Therapy Assessed reference to a FHIR resource
.... 20.60 Coded Annotation Types
.... 20.61 Condition Inheritance Patterns
.... 20.62 DNA Change Type
.... 20.63 Evidence Level Examples
.... 20.64 Functional Effect Value Set
.... 20.65 Genetic Therapeutic Implications
.... 20.66 Genomic Study Change Type ValueSet
.... 20.67 Genomic Study Data Format ValueSet
.... 20.68 Genomic Study Method Type ValueSet
.... 20.69 Genomic Study Status ValueSet
.... 20.70 Genomic Study Type ValueSet
.... 20.71 HUGO Gene Nomenclature Committee Gene Names (HGNC)
.... 20.72 Human Genome Variation Society (HGVS) Nomenclature
.... 20.73 Molecular Biomarker Categories
.... 20.74 Molecular Biomarker Codes
.... 20.75 Molecular Consequence Value Set
.... 20.76 Sequence Phase Relationships
.... 20.77 To Be Determined Value Set
.... 20.78 Variant Confidence Status
.... 20.79 ClinVar Evidence Level Example Codes
.... 20.80 Coded Annotation Type Codes
.... 20.81 Genomic Study Change Type CodeSystem
.... 20.82 Genomic Study Data Format CodeSystem
.... 20.83 Genomic Study Method Type CodeSystem
.... 20.84 Genomic Study Status CodeSystem
.... 20.85 Genomic Study Type CodeSystem
.... 20.86 Molecular Biomarker Ontology Codes
.... 20.87 PharmGKB Evidence Level Example Codes
.... 20.88 Sequence Phase Relationship Codes
.... 20.89 To Be Determined Codes
.... 20.90 Variant Confidence Status Codes
.... 20.91 DNA Change Type Map
.... 20.92 Genomic Study Status Map
.... 20.93 analysisTumorNormalDNA
.... 20.94 analysisTumorRNA
.... 20.95 AnnotationExample
.... 20.96 ATR-insertion-molc
.... 20.97 ATR-insertion-significance
.... 20.98 ATR-insertion-var
.... 20.99 bundle-CG-IG-HLA-FullBundle-01
.... 20.100 bundle-cgexample
.... 20.101 bundle-cgexample-withGrouping
.... 20.102 bundle-complexVariant-nonHGVS
.... 20.103 bundle-compound-heterozygote
.... 20.104 bundle-CYP2C19
.... 20.105 bundle-oncology-diagnostic
.... 20.106 bundle-oncology-report-example
.... 20.107 bundle-oncologyexamples-r4
.... 20.108 bundle-oncologyexamples-r4-withGrouping
.... 20.109 bundle-pgxexample
.... 20.110 bundle-sequence-phase-relation-CYP2C19
.... 20.111 CGPatientExample01
.... 20.112 CNVAnalysis-called
.... 20.113 denovoChild
.... 20.114 denovoFather
.... 20.115 denovoMother
.... 20.116 diagnosticImplication-interact-smn1-smn2
.... 20.117 diagnosticreport-hla-glstring-r4
.... 20.118 EGFR-L858R-molc
.... 20.119 EGFR-L858R-significance
.... 20.120 EGFR-L858R-therapuDrug1
.... 20.121 EGFR-L858R-therapuDrug2
.... 20.122 EGFR-L858R-var
.... 20.123 eMERGEServiceRequest
.... 20.124 ExampleGermlineCNV
.... 20.125 ExampleGermlineDEL
.... 20.126 ExampleGermlineINV
.... 20.127 ExampleLab
.... 20.128 ExampleOrg
.... 20.129 ExamplePatient
.... 20.130 ExampleServiceRequest
.... 20.131 ExampleSomaticCNV
.... 20.132 ExampleSomaticDEL
.... 20.133 ExampleSomaticINV
.... 20.134 ExampleSpecimen
.... 20.135 FindALLPopulationSpecificVariantsOutput
.... 20.136 FindANYPopulationSpecificVariantsOutput
.... 20.137 FindPopulationDxImplicationsOutput
.... 20.138 FindPopulationMolecConseqOutput
.... 20.139 FindPopulationSpecificHaplotypesOutput
.... 20.140 FindPopulationStructuralIntersectingVariantsOutput
.... 20.141 FindPopulationStructuralSubsumingVariantsOutput
.... 20.142 FindPopulationTxImplicationsOutput
.... 20.143 FindStudyMetadataOutput
.... 20.144 FindSubjectDxImplicationsOutput
.... 20.145 FindSubjectHaplotypesOutput
.... 20.146 FindSubjectMolecConseqOutput
.... 20.147 FindSubjectSpecificHaplotypesOutput
.... 20.148 FindSubjectSpecificVariantsOutput
.... 20.149 FindSubjectStructuralIntersectingVariantsOutput
.... 20.150 FindSubjectStructuralSubsumingVariantsOutput
.... 20.151 FindSubjectTxImplicationsOutput
.... 20.152 FindSubjectVariantsOutput
.... 20.153 FullGenome-GRCh38
.... 20.154 genomicFileFatherBAM
.... 20.155 genomicFileMotherBAM
.... 20.156 genomicFileProbandBAM
.... 20.157 genomicFileProbandVCF
.... 20.158 genomicPatient
.... 20.159 GenomicReportExample01
.... 20.160 genomicServiceRequest
.... 20.161 GenomicServiceRequestExample01
.... 20.162 genomicSpecimen
.... 20.163 GenomicSpecimenExample01
.... 20.164 GenomicSpecimenExample02
.... 20.165 genomicstudy-trio2
.... 20.166 genomicstudyanalysis-trio2
.... 20.167 genomicVCFfile-cnv
.... 20.168 genomicVCFfile-simple
.... 20.169 Genotype-Clinical-Trial-Example-using-haplotypes
.... 20.170 genotype-hla-a-glstring-r4
.... 20.171 GenotypeExample1
.... 20.172 GenotypeExamplePharmVar
.... 20.173 GenRiskDiabetesT2
.... 20.174 GrouperEx01
.... 20.175 GrouperEx02
.... 20.176 GrouperEx03
.... 20.177 haplotype-hla-a-1-r4
.... 20.178 HaplotypeExamplePharmVar01
.... 20.179 HaplotypeExamplePharmVar02
.... 20.180 HaplotypeSet-Clinical-Trial-Example-1of2
.... 20.181 HaplotypeSet-Clinical-Trial-Example-2of2
.... 20.182 HER2byImmuneStainExample
.... 20.183 HER2byImmunoassayExample
.... 20.184 HG00403
.... 20.185 HLA-A-haplotype1
.... 20.186 HLA-A-haplotype2
.... 20.187 HLA-B-haplotype1
.... 20.188 HLA-B-haplotype2
.... 20.189 HLA-C-haplotype1
.... 20.190 HLA-C-haplotype2
.... 20.191 ISCN-CMLExample
.... 20.192 ISCN-CMLImplication
.... 20.193 ISCN-NormalExample
.... 20.194 lungMass
.... 20.195 lungMass-analysis1
.... 20.196 lungMass-analysis2
.... 20.197 MedicationRecommendationExample1
.... 20.198 MedicationStatementWarfarin
.... 20.199 MicrosatelliteInstabilityExample01
.... 20.200 molec-conseq1
.... 20.201 molec-conseq2
.... 20.202 molec-conseq3
.... 20.203 molec-conseq4
.... 20.204 MSH2-del-disease
.... 20.205 MSH2-del-molc
.... 20.206 MSH2-del-var
.... 20.207 MSIExample
.... 20.208 MultipleRepeatExpansions
.... 20.209 normalSpecimen
.... 20.210 NOTCH1-significance
.... 20.211 NOTCH1-uncertain-molc
.... 20.212 NOTCH1-uncertain-var
.... 20.213 NTHL1-snv-disease
.... 20.214 NTHL1-snv-molc
.... 20.215 NTHL1-snv-var
.... 20.216 obs-idh-ex
.... 20.217 obs1-interact-smn1-smn2
.... 20.218 obs2-interact-smn1-smn2
.... 20.219 orderingPractitioner
.... 20.220 pathologistPractitioner
.... 20.221 PDL1Example
.... 20.222 performingOrganization
.... 20.223 Pgx-geno-1001
.... 20.224 Pgx-geno-1002
.... 20.225 Pgx-geno-1003
.... 20.226 Pgx-var-1011
.... 20.227 Pgx-var-1012
.... 20.228 Pgx-var-1013
.... 20.229 Pgx-var-1014
.... 20.230 Pgx-var-1015
.... 20.231 Pgx-var-1016
.... 20.232 Pgx-var-1017
.... 20.233 Pgx-var-1018
.... 20.234 Pgx-var-1019
.... 20.235 Pgx-var-1020
.... 20.236 Pgx-var-1021
.... 20.237 PGxGenomicReportEMERGE
.... 20.238 PGxGenomicReportEMERGE-withGrouping
.... 20.239 PGXGenomicStudy
.... 20.240 PGXGenomicStudyAnalysis
.... 20.241 PGxRecEx01
.... 20.242 PGxRecEx02
.... 20.243 PGxRecEx03
.... 20.244 PGxRecEx04
.... 20.245 PGxRecEx05
.... 20.246 PolyGenicDiagnosticImpExample
.... 20.247 practitioner02
.... 20.248 RepeatExpansion
.... 20.249 ROS1-Fusion
.... 20.250 ROS1-Fusion-disease
.... 20.251 ROS1-Fusion-therapuDrug
.... 20.252 ROS1-Fusion-therapuTrial
.... 20.253 ROS1-Fusion-var
.... 20.254 SequencePhaseRelationExample1
.... 20.255 SequencingProcedure
.... 20.256 servicerequest-hla-a-r4
.... 20.257 SimpleVariantAnalysis-called
.... 20.258 SNVexample
.... 20.259 somaticPatient
.... 20.260 somaticReport
.... 20.261 somaticServiceRequest
.... 20.262 somaticStudy
.... 20.263 somaticVCFfile
.... 20.264 specimen-hla-r4
.... 20.265 STAG2-insertion-molc
.... 20.266 STAG2-insertion-significance
.... 20.267 STAG2-insertion-var
.... 20.268 supervisorPractitioner
.... 20.269 Therapeutic-Implication-Clinical-Trial-2
.... 20.270 Therapeutic-Implication-Clinical-Trial-Somatic
.... 20.271 TherapeuticImplicationExample1
.... 20.272 therapuDrug1-interact-smn1-smn2
.... 20.273 therapuDrug2-interact-smn1-smn2
.... 20.274 therapuDrug3-interact-smn1-smn2
.... 20.275 TMB-therapuDrug
.... 20.276 TMBExample
.... 20.277 triodenovo-software
.... 20.278 TumorMutationBurdenExample01
.... 20.279 tumorSpecimen
.... 20.280 TxImp01
.... 20.281 TxImp02
.... 20.282 TxImp03
.... 20.283 TxImp04
.... 20.284 TxImp05
.... 20.285 TxImp06
.... 20.286 UncallableRegions
.... 20.287 Variant-Somatic-Clinical-Trial
.... 20.288 variant-with-molec-consequences
.... 20.289 VariantExample
.... 20.290 VariantExample1
.... 20.291 VariantExample2
.... 20.292 WES-FullSequencedRegion-GRCh38
.... 20.293 WES-UncallableRegions-GRCh38
.... 20.294 ZFHX3-significance
.... 20.295 ZFHX3-uncertain-molc
.... 20.296 ZFHX3-uncertain-var